Zebrafish mutagenesis screens hold promise for identifying genes underlying phenotypes relevant to development and to disease. Associating phenotype and genotype will require development of genotyping tools matched in throughput to the scale of these screens. This proposal addresses this gap in response to the program announcement "Tools for Genetic Studies in Zebrafish." We propose to apply our extensive experience in high-throughput genotyping to create a shared genome-wide mapping resource for the zebrafish community. The Principal Investigator has developed state-of-the-art genotyping technologies and informatics tools that are currently operational and directly applicable in zebrafish mapping. We have completed approximately one million genotypes, developed >75 fluorescent simple tandem repeat (STR) marker panels (including a robust genome-wide set for human genetic mapping), discovered and genotyped comprehensive single nucleotide polymorphisms (SNP) maps across candidate genes in large-scale human studies, and are now performing a genome-wide mouse SNP scan. Here we propose development of shared zebrafish mapping resources: robust genome-wide marker sets for high-throughput genetic screens, and a public bioinformatics system to organize and design custom assays for subsequent fine mapping.